lazappi / ozsinglecell2019

Analysis of the Swarbrick dataset for the Oz Single Cell Challenge 2019

Oz Single Cells 2019

Analysis of the Swarbrick dataset for the Oz Single Cells Challenge 2019.

Started 2019-07-19.

A workflowr project.

Directory structure

• R - Resuable R code (functions etc.)
• analysis - R Markdown analysis files
• docs - Rendered workflowr website
• data - Raw data used for analysis
• output - Output files
• packrat - packrat files

Data

Input data files include:

• Swarbrick-SCE.Rds - Swarbrick data as a SingleCellExperiment object downloaded from the challenge website and converted from .Rdata. to .Rds
• Swarbrick-CITE.csv.gz - Swarbrick CITE data downloaded from the challenge website, compressed and with the first column renames as "Antibody"
• antibody_genes.tsv - Mapping of antibodies to genes (manually complied)

Additional intermediate data files are produced by analysis files. These are numbered according to the file that produced them.

Analysis

Current analysis files include:

• _site.yaml - Website configuration file
• about.Rmd - About page
• index.Rmd - Index page
• license.Rmd - License page
• 01-pre-processing.Rmd - Basic pre-processing of the dataset
• 02-quality-control.Rmd - Quality control of the dataset
• 03-comparison.Rmd - Comparison of antibody and gene expression
• 04-clustering.Rmd - Clustering of the RNA-seq dataset
• 05-cite-clustering.Rmd - Clustering of the CITE dataset
• 06-cluster-comparison.Rmd - Comparison of RNA and CITE clustering results

Code

Current code files include:

• annotate.R - Functions for annotating SingleCellExperiment objects
• plotting.R - Plotting functions
• crossover.R - Functions for comparing results
• output.R - Functions for nicely formatting output
• set_paths.R - Set file paths to data objects
• setup_knitr.R - Set default knitr options.

Output

Output files are saved in directories according the file that produced them. See the summary at the end of each analysis file for descriptions.